The Doctor is waiting to meet an army in the Swiss Alps when a force of Gauls attack. The Gauls are defeated, and the Doctor and his "cabinet" are taken captive by the army — the Carthaginians, led by Hannibal and his talking elephant, Surus, who are on their way to invade Rome. They believe the Doctor is a Roman spy, especially when he reveals he knows all about their plans. The Doctor refuses to tell Hannibal what to do or what the Romans know.

At the same time, in his rooms on Gallifrey, the Doctor is disturbed by his artificial manservant Badger, who brings him the news. The Doctor takes no notice of the local politics and instead reviews news of the galaxy, noting with dismay that the Thalek Empire continues to expand with no-one doing anything about it. He also discovers Badger, acting on his usual instructions, has declined an invitation to attend a Presidential reception celebrating the 300th anniversary of his book, An Adventure in Time and Space. Badger tries to hypnotise him into taking more interest in politics, but fails.

The Doctor is then visited by his great-granduncle, Ordinal-General Quences, who expresses disapproval at the Doctor's writing, and reiterates an old argument that the Doctor is wasting his potential and a great disappointment to the family. To Quences' surprise, the Doctor responds by transporting them both to the Capitol, where the Doctor is being invested as the new President of the High Council of Time Lords. Quences is at first very pleased, but soon shows a darker side when he speaks of the importance of the "tradition" that each President dies in office, showing the transient nature of power. Disturbed, the Doctor reveals that the inauguration is a projection, created using a possibility generator he uses to conduct research.

As Quences and the Doctor resume arguing, there's a knock at the door and the Doctor sends Badger to turn away the visitor. The visitor will not be dissuaded, however, and shoots Badger — it's Susan, the Doctor's granddaughter. Badger recovers and as Susan retreats into the room, she finds the Doctor seemingly unconscious and connected to a machine; she touches him and enters the possibility projection of the Swiss Alps, where the Doctor has seemingly been all along. Quences appears and angrily orders Badger to follow Susan.

Inside the projection, the Doctor reveals to Hannibal that he created them all as research for his next novel, but perhaps hadn't done enough research of his own; the army is dying in the cold, unsure how to proceed, and the Doctor wonders whether he has a duty to intervene for their sake. Susan and Badger are brought to the camp, having been found by Surus, by the Doctor doesn't recognise her. Allowed to speak alone on the promise of telling Hannibal what he should do, Susan tells the Doctor of his family, and that she has grandchildren of his own who love his books. The Doctor's memories return and he wonders if he has made a mistake hiding away in his possibility generator, researching his adventures, and whether he should have acted on his long ago plan to steal a TARDIS and leave Gallifrey with Susan...but he realises she is hiding something.

Susan leaves the Alps possibility, and the Doctor accompanies her, but before they can leave his rooms Badger tries to stop them. Susan realises the servant has a hypnotic hold over the Doctor, and as she tries to help him escape Quences appears, having discovered Susan's secret: she is shortly to be made President of the High Council. Susan is shocked by his arrival, as Quences died long ago, when she was still a girl. Susan's revelation breaks the hypnotic hold on the Doctor, and he realises Quences illegally transferred his consciousness not into the Matrix, but instead into Badger — it was Quences who gave the servant to the Doctor.

The Doctor escapes with Susan back into the possibility generator, this time taking the controls with him to prevent outside interference. They arrive on the other side of the Alps, and must wait for Hannibal's army to arrive if they are to leave. Susan reveals she has sent many letters, and now realises that the brusque replies were sent by Badger to keep her away from the Doctor. Despite this she has learned from her Grandfather, and wants to be President not for family reasons, but to reinvigorate Time Lord society. The Doctor promises to help her, but when the Carthaginians arrive, they have suffered great losses; Hannibal, dissatisfied with the Doctor's advice, has sought help from Quences, who has entered the possibility generator with the help of Badger.

The Doctor tries to give Hannibal advice before retrieving his cabinet — his TARDIS — and leaving with Susan, reluctantly agreeing to take Badger, though Susan thinks she's seen Quences (or someone like him) in old archive records. The cabinet, however, is just that — an empty box — since it was only a literary device. The Doctor realises his imagination is in control of the possibility generator, however, and whisks himself and Susan away to a rose garden. There, the wearied and confused Doctor nearly becomes lost in the infinite possibilities within the generator; in most of them the Time Lords remain aloof and do nothing to stop the evil in universe, but in one he sees himself and Susan stealing a TARDIS. Susan helps him navigate his way out of the infinity, and they return to his rooms.

However, Susan was thinking about Badger and Quences as they returned, and this allowed them a path to exit the generator too. She has realised his true identity: Auld Mortality, the living reminder that power is fleeting and that all things must end, and he has been present at the investiture of every President. If a family member — Susan — becomes President, Quences will achieve ultimate power.

The return to the Panopticon, as it is time for Susan's investiture; Quences whispers in her ear, as he has for every President, but this time the Doctor is whispering in Quences' ear too. Now President, Susan tries to use her power to banish Auld Mortality, and the Doctor addresses the council, warning them about Quences' corruption. Quences orders Badger to kill the Doctor, but the servant hesitates, and in that moment Hannibal and his army — thanks to the Doctor's previous advice — exit the possibility generator and storm the Panopticon. Surus destroys Badger, causing Quences to flicker out of existence, and the curse of Auld Mortality to be lifted.

Back in his quarters, the Doctor bids Hannibal farewell as his army returns to their possibility, noting sadly that they will die in their war. Describing the generator as dangerous, Susan switches it off, overcoming the Doctor's fear that she is just a possibility too. This clears the Doctor's mind, and he realises his rooms are really the console room of the TARDIS he planned to steal all those years ago. Susan encourages him to leave Gallifrey now while he has the chance, and he invites her to join him.

Perhaps she does; perhaps she doesn't. There are so many possibilities...

There are many similarities between this story and Deadline, another audio drama in the Unbound series. Both stories are about a struggling writer penning stories about travels in time and space as the Doctor, and being reunited with a family member as they begin to get fiction and reality confused. They also both feature alternate First Doctors. However, in Auld Mortality, the main character actually was the Doctor, whereas Martin Bannister just believes himself to be. In a way, that story could be seen as a dark parody of this one. That story's ending is a dark mirror of this story's, with Martin believing himself to be leaving in the TARDIS with Susan, as the Doctor did in this story, as he in reality suffocates to death in a wardrobe. The TARDIS being disguised as a wardrobe is also mentioned in Auld Mortality as a theoretical possibly.